In anti-seepage engineering, quality control and engineering applications are based on the accurate measurement of seepage indices for low-permeability materials. The test used to determine the seepage indices for low-permeability materials adopts an external source to produce water pressure, and the seepage flux produced during the process requires manual measurement; thus, the apparatus used is complex and difficult to operate, thereby lowering the testing efficiency and restricting its application. In this study, a built-in servo motor was used to produce high water pressure with a pressure transmitter, and it controlled and measured the seepage pressure. According to the rotation number of the electric cylinder motor, the volume change of water in the hydraulic cylinder was calculated and, thus, the seepage flux was deduced. A simple fully automatic seepage apparatus for low-permeability materials was designed with a human–computer interface. The results showed the successful calculation of seepage flux as a function of the rotation number of the servo motor through automatic measurement. Furthermore, the replacement of the external high-pressure source with the built-in servo motor enhanced the safety performance, and the human–computer interface enabled an interactive operation and simplified the measurement structure. This simple testing method can provide technical support for quality inspection and construction control of anti-seepage engineering.